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Visualisation

The program visTraj, similar to the planes program from the SOM_PAK package, was developed to show the trajectory (or order) of the input vectors through the map. Figures 5.2 and 5.3 show examples of the output from visTraj where the trajectory is simply the carbon-$\alpha$ trace. The map units (represented by grey circles) are arranged in an $M \times N$ array with the origin at the top left. The trajectory is coloured from blue (this may appear as a deep purply blue) at the start (N-terminus) to red at the end (C-terminus), passing through green and yellow on the way. Individual data points (nodes) are represented by circles. To avoid uninterpretable trajectories where paths overlap, nodes are not drawn in the centre of the map units (as in planes), but at an angle and distance proportional to $i$ and $q_i$ (quantisation error for input vector $v_i$) respectively. Therefore it is important to ignore the position of a node within a circle, except to distinguish it from another node.